glennhickey
commented
11 months ago The easiest thing to try would be using -B. This way it will call something homozygous only if it has 6X the depth of the next best allele. The factor can be adjusted with -b.
By default it uses a Poisson model based on background depth and a baseline error rate. You can try decreasing this (-e) to see if it helps.
I think there's an underlying issue where these parameters were tuned on coverage in the 20-50X range, obviously aren't scaling well to your 1000X plus data.
brodie-mumphrey
1. What were you trying to do?
Use
vg callto genotype a graph.2. What did you want to happen?
Have heterozygous variants called as heterozygous.
3. What actually happened?
Variants were called homozygous despite hundreds of reads supporting both alleles. One allele has significantly less allele support due to allelic imbalance, so I understand that it may deviate further than expected from the neutral 50/50 expectation. Are there options to adjust this so that lower allelic fraction variants can still be called? Example output for a few affected variants:
4. If you got a line like
Stack trace path: /somewhere/on/your/computer/stacktrace.txt, please copy-paste the contents of that file here:5. What data and command can the vg dev team use to make the problem happen?
6. What does running
vg versionsay?